[gmx-users] question about image

Weihua Guo whguo at midway.uchicago.edu
Fri Mar 19 21:05:01 CET 2004

Hi gmx-users,

I have two peptides binding together, centered in the box and solvated as 
my starting point. Now after several nanoseconds they drifted close to the
side, and suddenly one chain sticks out of the box and get imaged in the
other direction. I am sure it is due to image. They are imaged
seperately during the run. I viewed the pdb file generated by "editconf -f
x.gro -o x.pdb" with rasmol. (I used octahedron box and it showed me a
cubic box though)

My question is: Is the dynamics (energy terms etc) still correct? If it
is, how should I treat the x.gro file in order for rasmol to show the
actual orientations? 


Weihua Guo
Department of Chemistry
The University of Chicago
5735 S Ellis Ave 
Chicago, IL 60637

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